SEARCH

SEARCH BY CITATION

References

  • Abell GCJ & Bowman JP (2005) Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiol Ecol 51: 265277.
  • Alonso C & Pernthaler J (2006) Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. Environ Microbiol 8: 20222030.
  • Alonso-Sáez LV , Balague EL , Sa O , Sanchez JM , Gonzale J , Pinhassi et al. (2007) Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH. FEMS Microbiol Ecol 60: 98112.
  • Amann RI , Binder BJ , Olson RJ , Chisholm SW , Devereux R & Stahl DA (1990) Combination of 16S ribosomal-RNA-targeted oligonucleotide probes with flow-cytometry for analyzing mixed microbial-populations. Appl Environ Microbiol 56: 19191925.
  • Arrieta JM , Weinbauer MG , Lute C & Herndl GJ (2004) Response of bacterioplankton to iron fertilization in the Southern Ocean. Limnol Oceanogr 49: 799808.
  • Bano N & Hollibaugh JT (2002) Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl Environ Microbiol 68: 505518.
  • Boetius A , Ravenschlag K , Schubert CJ , Rickert D , Widdel F , Gieseke A , Amann R , Jorgensen BB , Witte U & Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623626.
  • Bowman JP & McCuaig RD (2003) Biodiversity community structural shifts and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69: 24632483.
  • Brown SL & Landry MR (2001) Microbial community structure and biomass in surface waters during a Polar Front summer bloom along 170 degrees W. Deep-Sea Res II 48: 40394058.
  • Chao A (1984) Nonparametric-estimation of the number of classes in a population. Scand J Stat 11: 265270.
  • Church MJ , DeLong EF , Ducklow HW , Karner MB , Preston CM & Karl DM (2003) Abundance and distribution of planktonic Archaea and Bacteria in the waters west of the Antarctic Peninsula. Limnol Oceanogr 48: 18931902.
  • Clarke KR & Warwick RM (2001) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation, 2nd edn. PRIMER-E, Plymouth.
  • Corzo A , Rodriguez-Galvez S , Lubian L , Sobrino C , Sangra P & Martinez A (2005) Antarctic marine bacterioplankton subpopulations discriminated by their apparent content of nucleic acids differ in their response to ecological factors. Polar Biol 29: 2739.
  • Cottrell MT & Kirchman DL (2000) Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 66: 51165122.
  • Crump BC , Hopkinson CS , Sogin ML & Hobbie JE (2004) Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl Environ Microbiol 70: 14941505.
  • Delille D (2003) Seasonal and inter-annual variability of bacterioplankton biomass at station Kerfix off Kerguelen Islands Antarctica. Oceanol Acta 26: 225229.
  • Delille D & Rosiers C (1996) Seasonal changes of Antarctic marine bacterioplankton and sea ice bacterial assemblages. Polar Biol 16: 2734.
  • Delong EF , Franks DG & Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs free-living marine bacterial assemblages. Limnol Oceanogr 38: 924934.
  • Ducklow H , Carlson C , Church M , Kirchman D , Smith D & Steward G (2001) The seasonal development of the bacterioplankton bloom in the Ross Sea Antarctica 1994-1997. Deep-Sea Res II 48: 41994221.
  • Dutton CM , Paynton C & Sommer S (1993) General method for amplifying regions of very high G + C content. Nucleic Acids Res 21: 29532954.
  • Elderfield H (1972) Effects of volcanism on water chemistry, Deception Island, Antarctica. Mar Geol 13: M1M6.
  • Fandino LB , Riemann L , Steward GF , Long RA & Azam F (2001) Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing. Aquat Microb Ecol 23: 119130.
  • Fuerst JA (1995) The planctomycetes: emerging models for microbial ecology, evolution, and cell biology. Microbiology 141: 14931506.
  • Fuhrman JA , Steele JA , Hewson I , Schwalbach MS , Brown MV , Green JL & Brown JH (2008) A latitudinal diversity gradient in planktonic marine bacteria. PNAS 105: 77747778.
  • Gafan GP & Spratt DA (2005) Denaturing gradient gel electrophoresis gel expansion (DGGEGE) – an attempt to resolve the limitations of co-migration in the DGGE of complex polymicrobial communities. FEMS Microbiol Lett 253: 303307.
  • Gentile G , Giuliano L , D'Auria G , Smedile F , Azzaro M , De Domenico M & Yakimov MM (2006) Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing. Environ Microbiol 8: 21502161.
  • Giovannoni SJ & Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 437: 343348.
  • Giovannoni SJ , Tripp HJ , Givan S , Podar M , Vergin KL , Baptista D et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 12421245.
  • Glöckner FO , Fuchs BM & Amann R (1999) Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65: 37213726.
  • Glöckner FO , Zaichikov E , Belkova N , Denissova L , Pernthaler J , Pernthaler A & Amann R (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Appl Environ Microbiol 66: 50535065.
  • Gonzalez JM , Simo R , Massana R , Covert JS , Casamayor EO , Pedros-Alio C & Moran MA (2000) Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl Environ Microbiol 66: 42374246.
  • Good IL (1953) The population frequencies of species and the estimation of population parameters. Biometrika 80: 193201.
  • Grzymski JJ , Carter BJ , DeLong EF , Feldman RA , Ghadiri A & Murray AE (2006) Comparative genomics of DNA fragments from six antarctic marine planktonic bacteria. Appl Environ Microbiol 72: 15321541.
  • Hall T (1999) A user-friendly biological sequence alignment editor for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 9598.
  • Helms C (1990) Method: denaturing gradient gel electrophoresis (DGGE). http://hdklab.wustl.edu/lab_manual/dgge/dgge1.html%25 accessed 5 January 2008
  • Hendry KR , Rickaby REM & Allen CS (2011) Changes in micronutrient supply to the surface Southern ocean (Atlantic Sector) across the glacial termination. Geochem Geophys Geosystems 12: Q09007, 11 pp. doi: 10.1029/2011GC003691.
  • Jackson CR , Roden EE & Churchill PF (2000) Denaturing gradient gel electrophoresis can fail to separate 16S rDNA fragments with multiple base differences. Mol Biol Today 1: 4951.
  • Kirchman DL (2001) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39: 91100.
  • Korb RE , Whitehouse MJ , Thorpe SE & Gordon M (2005) Primary production across the Scotia Sea in relation to the physico-chemical environment. J Mar Syst 57: 231249.
  • Liu CL & Shao ZZ (2005) Alcanivorax dieselolei sp nov a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 55: 11811186.
  • Longnecker K , Sherr BF & Sherr EB (2005) Activity and phylogenetic diversity of high and low nucleic acid content, and ETS-active, bacterial cells in an upwelling ecosystem. Appl Environ Microbiol 71: 77377749.
  • Malmstrom RR , Straza TRA , Cottrell MT & Kirchman DL (2007) Diversity abundance and biomass production of bacterial groups in the western Arctic Ocean. Aquat Microb Ecol 47: 4555.
  • Manz W , Amann R , Ludwig W , Wagner M & Schleifer KH (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria – problems and solutions. Syst Appl Microbiol 15: 593600.
  • Manz W , Amann R , Ludwig W , Vancanneyt M & Schleifer KH (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroidetes in the natural environment. Microbiology 142: 10971106.
  • Meier H , Amann R , Ludwig W & Schleifer KH (1999) Specific oligonucleotide probes for in situ detection of a major group of Gram-positive bacteria with low DNA G+C content System. Appl Microbiol 22: 186196.
  • Moore JK & Abbott MR (2002) Surface chlorophyll concentrations in relation to the Antarctic Polar Front: seasonal and spatial patterns from satellite observations. J Mar Syst 37: 6986.
  • Moreira D , Rodriguez-Valera F & Lopez-Garcia P (2006) Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group. Microbiology 152: 505517.
  • Morris RM , Longnecker K & Giovannoni SJ (2006) Pirellula and OM43 are among the dominant lineages identified in an Oregon coast diatom bloom. Environ Microbiol 8: 13611370.
  • Murphy EJ , Watkins JL , Trathan PN et al. (2007) Spatial and temporal operation of the Scotia Sea ecosystem: a review of large-scale links in a krill centred food web. Philos Trans R Soc Lond B Biol Sci 362: 113148.
  • Murray AE & Grzymski JJ (2007) Diversity and genomics of Antarctic marine micro-organisms. Philos Trans R Soc Lond B Biol Sci 362: 22592271.
  • Murray AE , Wu KY , Moyer CL , Karl DM & DeLong EF (1999) Evidence for circumpolar distribution of planktonic Archaea in the Southern Ocean. Aquat Microb Ecol 18: 263273.
  • Neef A , Amann R , Schlesner H & Schleifer KH (1998) Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144: 32573266.
  • O'Sullivan LA , Weightman AJ & Fry JC (2002) New degenerate Cytophaga-Flexibacter-Bacteroidetes-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon. Appl Environ Microbiol 68: 201210.
  • Øvreås L , Forney L , Daae FL & Torsvik V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63: 33673373.
  • Pearce DA (2008) Biodiversity of the bacterioplankton in the surface waters around Southern Thule in the Southern Ocean. Ant Sci 20: 291300.
  • Pinhassi J , Gomez-Consarnau L , Alonso-Saez L , Sala MM , Vidal M , Pedros-Alio C & Gasol JM (2006) Seasonal changes in bacterioplankton nutrient limitation and their effects on bacterial community composition in the NW Mediterranean Sea. Aquat Microb Ecol 44: 241252.
  • Pizzetti I , Gobet A , Fuchs BM , Amann R & Fazi S (2011a) Abundance and diversity of Planctomycetes in a Tyrrhenian coastal system of central Italy. Aquat Microb Ecol 65: 129141.
  • Pizzetti I , Fuchs BM , Gerdts G , Wichels A , Wiltshire KH & Amann R (2011b) Temporal variability of coastal Planctomycetes clades at Kabeltonne Station, North Sea. Appl Environ Microbiol 77: 50095017.
  • Pommier T , Pinhassi J & Hagström Å (2005) Biogeographic analysis of ribosomal RNA clusters from marine bacterioplankton. Aquat Microb Ecol 41: 7989.
  • Pommier T , Canback B , Riemann L , Bostrom KH , Simu K , Lundberg P , Unlid A & Hagström Å (2007) Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16: 867880.
  • Porter KG & Feig YS (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25: 943948.
  • Riemann L , Leitet C , Pommier T , Simu K , Holmfeldt K , Larsson U & Hagström Å (2008) The native bacterioplankton community in the central Baltic sea is influenced by freshwater bacterial species. Appl Environ Microbiol 74: 503515.
  • Sanchez O , Gasol JM , Massana R , Mas J & Pedros-Alio C (2007) Comparison of different denaturing gradient gel electrophoresis primer sets for the study of marine bacterioplankton communities. Appl Environ Microbiol 73: 59625967.
  • Sekiguchi H , Tomioka N , Nakahara T & Uchiyama H (2001) A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis. Biotechnol Lett 23: 12051208.
  • Selje N , Simon M & Brinkhoff T (2004) A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427: 445448.
  • Simon M , Glöckner FO & Amann R (1999) Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean. Aquat Microb Ecol 18: 275284.
  • Sloyan BM (2005) Spatial variability of mixing in the Southern Ocean. Geophys Res Lett 32: L18603, doi: 10.1029/2005GL023568.
  • Stahl DA & Amann R (1991) Development and application of nucleic acid probes. Nucleic Acid Techniques in Bacterial Systematics ( Stackebrandt E & Goodfellow M , eds), pp. 205248. John Wiley & Sons Ltd, Chichester.
  • Staley JT & Gosink JJ (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annu Rev Microbiol 53: 189215.
  • Topping JN , Heywood JL , Ward P & Zubkov MV (2006) Bacterioplankton composition in the Scotia Sea Antarctica during the austral summer of 2003. Aquat Microb Ecol 45: 229235.
  • Venter JC , Remington K , Heidelberg JF et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 6674.
  • Vergin KL , Urbach E , Stein JL , DeLong EF , Lanoil BD & Giovannoni SJ (1998) Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl Environ Microbiol 64: 30753078.
  • Wallner G , Amann R & Beisker W (1993) Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14: 136143.
  • Weitz M , Gram L , Jorgensen B & Schramm A (2010) Latitudinal patterns in the abundance of major marine bacterioplankton groups. Aquat Microb Ecol 61: 179189.
  • West NJ , Obernosterer I , Zemb O & Lebaron P (2008) Major differences of bacterial diversity and activity inside and outside of a natural iron-fertilized phytoplankton bloom in the Southern Ocean. Environ Microbiol 10: 738756.
  • Zdanowski MK & Figuerias FG (1997) Relationships between the abundance of bacteria and other biota and the hydrographic variability in the Ria de Vigo, Spain. Mar Ecol Prog Ser 147: 257267.
  • Zhang JW & Zeng RY (2007) Psychrotrophic amylolytic bacteria from deep sea sediment of Prydz Bay, Antarctic: diversity and characterization of amylases. World J Microbiol Biotechnol 23: 15511557.
  • Zubkov MV , Fuchs BM , Archer SD , Kiene RP , Amann R & Burkill PH (2001) Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ Microbiol 3: 304311.
  • Zubkov MV , Fuchs BM , Tarran GA , Burkill PH & Amann R (2002) Mesoscale distribution of dominant bacterioplankton groups in the northern North Sea in early summer. Aquat Microb Ecol 29: 135144.